Team:Panama/Modeling

From 2010.igem.org

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* Venue:  INDICASAT
* Venue:  INDICASAT
* Description: We identify a simple project based on past iGEM work and do our first BioBrick protocol project. Nothing innovative, but an opportunity to practice the protocols.
* Description: We identify a simple project based on past iGEM work and do our first BioBrick protocol project. Nothing innovative, but an opportunity to practice the protocols.
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===Meeting June 26===
 
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At this moment we have two ideas for develop.  We are debating which idea is more feasible.
 
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Idea #1:  Carlos´s  team idea
 
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We want to produce Rhamnolipid in bacteria (e.coli) to use it as a biosurfactant.
 
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First we have to be sure that our idea is not the same that the idea published in the reference paper.
 
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We want to make a biobrick to produce Rh1.
 
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We have to see how we can isolate the rhamnolipid, and be sure that the translation is functional.
 
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<gallery>
<gallery>
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Image:ErnestoIdea.jpg|Ernesto's Idea
 
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Image:P1000625.JPG |Panama Team
</gallery>
</gallery>
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Steps to follow:
 
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1.Amplified the Rhamnosyltransferase  1  complex from Pseudomona Auruginosa to clone the fragment. Size aprox 2.2 Kb.
 
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2.Ligation / Transformation
 
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3.Expression with reporter gen.
 
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4.Isolation
 
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5.Is the protein functional?
 
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6.Make sure that the rhamnolipid is produced in prescence of rhamnose and fatty acid.
 
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Notes:
 
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We can see the reaction ( enzymatic measure) by spectrometry.
 
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See kind of ligation.
 
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Decided if we are going to use sticky or blond ends. (Depend on the plasmid).
 
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But first, before the amplification we need to design our primers.
 
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Primers design:
 
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1.Check the gene sequence (In GenBank, FASTA format)
 
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2.Check the primer sequence.
 
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3.See kind of cloning.
 
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4.M13 tail for cleavage site.
 
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5.Look for cleavage site inside the rhamnosyltransferase 1 gene for our restriction enzymes.  We can´t cut our gene in the process.
 
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In summary the steps that we need to follow are:
 
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I.Primer design
 
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II.PCR or amplification
 
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III.Cloning
 
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IV.Expression
 
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V.Sequencing
 
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The most important steps are I and II. We need a good primers design and PCR if we want to have successful.
 
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Idea #2
 
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Ernesto team´s idea
 
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Production of Cecropin compound.  We want to produce the antibacterial cecropin compound. Naturally is produced by insects and plants.
 
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We want to use Anopheles gambiae cecropin precursor. The gene is about 550 pb.
 
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The steps to follow are the same in both groups.
 
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Both groups have to design the primers, and have all the experimental design for this week.
 
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1.The sequence of the interested gene.
 
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2.Design the primers. (50-100pb more at the begging and end of the sequence).
 
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3.Check for cloning sites. Which plasmid we are going to use, identify the restriction enzymes.
 
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4.Assemble the blocks. In paper assemble all the system. Promoter + Ribosomal binding site + interest gene + reporter gene + translation end site.
 
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All the design has to be on paper to analyze them and decided which idea is going to be the elected one.
 

Revision as of 20:59, 6 July 2010

IGEM Panama Team

Team_Panama

.

Contents

Notebook

DNA 101: Information store, replication. 26 May

  • Instructor: Dr. Abby Guerra
  • Date: 26 May 17h00-20h00
  • Venue: UTP
  • Description: A basic refresher course on how DNA stores information in the cell, and how it is involved in cellular replication.


DNA 102: Protein creation relationship to cellular function. 26 May

  • Instructor: Dr. Abby Guerra
  • Date: 26 May 17h00-20h00
  • Venue: UTP
  • Description: Introduction to how DNA drives cellular functions by creating proteins


DNA 103: DNA modification, plasmids

  • Instructor: Dr. Abby Guerra
  • Date: 26 May 17h00-20h00
  • Venue: UTP
  • Description:Introduction to long tested combinant DNA techniques, the role of plasmids in bacteria, and their use as a vector for DNA modification.


INDICASAT lecture: Drug discovery in nature

  • Instructor: Dr. Sergio Martinez
  • Date: (17h00-20h00 Thursday 3rd June)
  • Venue: INDICASAT
  • Description:Would be a brainstorming session as students start thinking about projects. It would be GREAT if we could take a molecule discovered by INDICASAT in coral/frogs/nature and put it in E. coli!...


INDICASAT lecture: Innovation

  • Instructor: Dr. Jagannatha Rao, Director of INDICASAT
  • Date: (17h30-20h00 Friday 4th June)
  • Venue: INDICASAT
  • Description: Dr. Rao's lecture on how to innovate.


DNA 104: BioBricks Protocol

  • Instructor: Sara/Patrick
  • Date: (17h30-20h00 Monday 7th June)
  • Venue: INDICASAT
  • Description: Introduction to the BrioBricks protocol


iGEM workshop follow up: Software tools

  • Instructor: Patrick / Sara
  • Date: (17h30-20h00 Monday 7th June)
  • Venue: INDICASAT
  • Description: Software tools available from the workshop.


iGEM workshop follow up: Safety, ethics

  • Instructor: Dr. Ricardo Lleonart
  • Date: (17h00-20h00 9th of June)
  • Venue: INDICASAT
  • Description: There is definetly a "safety considerations" requirement and we should address it early.


Wetlab 101: Tools of the lab and their use

  • Instructor: Dr. Patricia Llanes
  • Date: (17h00-20h00 9th June)
  • Venue: INDICASAT
  • Description: How to handle pipettes, clean test tubes, etc.


Wetlab 102: Let's raise a few E. coli

  • Instructor: Lorena Coronado and and Dr. Carmenza Spadafora
  • Date: (17h00-20h00 11th of June)
  • Venue: INDICASAT
  • Description: How does one handle E. coli?


Wetlab 103: Let's make an E. coli that fluoresce (or some simple BioBrick project)

  • Instructor: INDICASAT, Dr. Carmenza Spadafora
  • Date: (17h00-20h00 11th of June)
  • Venue: INDICASAT
  • Description: We identify a simple project based on past iGEM work and do our first BioBrick protocol project. Nothing innovative, but an opportunity to practice the protocols.

Panama Team

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